Thx. Nick. Will give it a shot. BTW, is there also a plan for using OPENMP, MKL or ATLAS to speed it up a bit? A lot of off the shelf rack mounted servers cannot put those cards in.
Gen On 8/17/10 10:03 AM, "Nick Schmansky" <ni...@nmr.mgh.harvard.edu> wrote: i forgot to add: make sure you have the latest nvidia driver, which has support for cuda 3. n. On Tue, 2010-08-17 at 13:00 -0400, Nick Schmansky wrote: > currently the _cuda binaries are distributed only in the centos4 and > centos4_x86_64 distributions. however, those should work in centos5, > and i've made a tarball of the _cuda binaries downloadable from here: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc > > look for the file 'fscudabins-linux-centos4_x86_64.tgz' and untar in > your freesurfer/bin dir. > > ! note ! this is a beta release of these binaries! they havent been > fully tested across a wide subject set, so don't use the -use-gpu flag > in any kind of important group analysis yet. > > please let of us know though of any problems you encounter. we need to > learn what kind of gpu cards people have out there in order to gauge how > far we can optimize our routines. > > n. > > On Tue, 2010-08-17 at 11:35 -0500, joel bruss wrote: > > Not to hijack your question, but I have similar questions. I have > > CUDA toolkit 3.1 installed, "cudadetect" returns: "Detecting CUDA... > > 32767 CUDA enabled device(s) detected." but, when I run recon-all, > > e.g.: > > > > recon-all -subjid PC -all -use-gpu > > > > > > I get the following errors at the mri_em_register_cuda step: > > > > /lcn2/lesion_warp.dir/MAP3_Nifti/freesurfer_subs.dir/PC/mri > > > > mri_em_register_cuda -skull > > nu.mgz /usr/freesurfer/average/RB_all_withskull_2008-03-26.gca > > transforms/talairach_with_skull.lta > > > > mri_em_register_cuda: Command not found. > > Linux linux-lvmb 2.6.34-12-desktop #1 SMP PREEMPT 2010-06-29 > > 02:39:08 +0200 x86_64 x86_64 x86_64 GNU/Linux > > > > A quick peak in /usr/freesurfer/bin shows that there is no > > mri_em_register_cuda binary. > > > > Are cuda binaries supposed to be bundled with the new 5.0 release, or > > are they created on the fly by FreeSurfer, or are they just plain > > missing? FWIW, I have CentOS 5 x86_64 version of FreeSurfer > > installed, running on OpenSuse 11.3 > > > > > > recon-all -s PC exited with ERRORS at Tue Aug 17 11:14:35 CDT 2010 > > > > > > On Tue, Aug 17, 2010 at 11:07 AM, Gennan Chen <gennan.c...@synarc.com> > > wrote: > > Hi! > > > > I will like to try the beta CUDA support in 5.0. And I have > > some questions here > > > > 1. Are all needed libraries bundled in the release? Or I > > need to go to CUDA's site to get those dependency? > > And if I need to, what are those dependency I need to > > grab and install? > > 2. I have RH 5 64 bit linux box with single NVIDIA FX > > card and macpro snow leopard box with dual NVIIDA GT > > 120. Does CUDA support work for both OS? If they do, > > any idea what the speed up will be?? > > > > Gen > > > > ______________________________________________________________ > > This email message is for the sole use of the intended > > recipient(s) and may contain confidential and privileged > > information. 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